[English] 日本語
Yorodumi- PDB-1ljw: Crystal Structure of Human Carbonmonoxy Hemoglobin at 2.16 A: A S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ljw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Carbonmonoxy Hemoglobin at 2.16 A: A Snapshot of the Allosteric Transition | ||||||
Components |
| ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Hemoglobin / R state / Allosteric / Carbonmonoxy / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.16 Å | ||||||
Authors | Safo, M.K. / Burnett, J.C. / Musayev, F.N. / Nokuri, S. / Abraham, D.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of human carbonmonoxyhemoglobin at 2.16 A: a snapshot of the allosteric transition. Authors: Safo, M.K. / Burnett, J.C. / Musayev, F.N. / Nokuri, S. / Abraham, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ljw.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ljw.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ljw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ljw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ljw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ljw_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1ljw_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/1ljw ftp://data.pdbj.org/pub/pdb/validation_reports/lj/1ljw | HTTPS FTP |
-Related structure data
Related structure data | 2hcoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | Asymmetric unit contains a dimer and the second dimer of the biological assembly is generate by the two fold axis: 1-Y, 1-X, 1/2-Z |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P69905 |
---|---|
#2: Protein | Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P68871 |
-Non-polymers , 4 types, 266 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.4 Details: Potassium phosphate, Sodium phosphate, toluene, hemoglobin, pH 6.4, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Perutz, M.F., (1968) J. Cryst. Growth, 2, 54. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 21, 2001 / Details: mirrors |
Radiation | Monochromator: MSC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→60 Å / Num. all: 14444 / Num. obs: 14444 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.16→2.26 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1229 / % possible all: 62.6 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. obs: 14441 / % possible obs: 90.2 % / Num. measured all: 44267 |
Reflection shell | *PLUS % possible obs: 92.6 % / Num. unique obs: 1229 / Num. measured obs: 2856 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2HCO Resolution: 2.16→60 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.2 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→60 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.16→2.21 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 60 Å / Num. reflection Rfree: 679 / % reflection Rfree: 5 % / Rfactor obs: 0.194 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.22 Å / Rfactor Rwork: 0.235 / Rfactor obs: 0.235 |